Fast Implementation of (Local) Population Stratification Methods

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Documentation for package ‘locStra’ version 1.9

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bed_fastCovEVs Computation of the k leading eigenvectors of the covariance matrix directly from a bed+bim+fam file.
bed_fastGrmEVs Computation of the k leading eigenvectors of the genomic relationship matrix, defined in Yang et al. (2011), directly from a bed+bim+fam file.
bed_fastJaccardEVs Computation of the k leading eigenvectors of the Jaccard similarity matrix directly from a bed+bim+fam file.. Note that this computation is only approximate and does not necessarily coincide with the result obtained by extracting the k leading eigenvectors of the Jaccard matrix computed with the function 'jaccardMatrix'.
bed_fastSMatrixEVs Computation of the k leading eigenvectors of the s-matrix (the weighted Jaccard similarity matrix) directly from a bed+bim+fam file. Note that in contrast to the parameters of the function 'sMatrix', the choice 'phased=FALSE' cannot be modified for the fast eigenvector computation. Moreover, inverting the minor allele is not possible when reading directly from external files.
covMatrix C++ implementation to compute the covariance matrix for a (sparse) input matrix. The function is equivalent to the R command 'cov' applied to matrices.
fastCovEVs Computation of the k leading eigenvectors of the covariance matrix for a (sparse) input matrix.
fastGrmEVs Computation of the k leading eigenvectors of the genomic relationship matrix, defined in Yang et al. (2011), for a (sparse) input matrix.
fastJaccardEVs Computation of the k leading eigenvectors of the Jaccard similarity matrix for a (sparse) input matrix. Note that this computation is only approximate and does not necessarily coincide with the result obtained by extracting the k leading eigenvectors of the Jaccard matrix computed with the function 'jaccardMatrix'.
fastSMatrixEVs Computation of the k leading eigenvectors of the s-matrix (the weighted Jaccard similarity matrix) for a (sparse) input matrix. Note that in contrast to the parameters of the function 'sMatrix', the choice 'phased=FALSE' cannot be modified for the fast eigenvector computation.
fullscan A full scan of the input data 'm' using a collection of windows given by the two-column matrix 'windows'. For each window, the data is processed using the function 'matrixFunction' (this could be, e.g., the 'covMatrix' function), then the processed data is summarized using the function 'summaryFunction' (e.g., the largest eigenvector computed with the function 'powerMethod'), and finally the global and local summaries are compared using the function 'comparisonFunction' (e.g., the vector correlation with R's function 'cor'). The function returns a two-column matrix which contains per row the global summary statistics (e.g., the correlation between the global and local eigenvectors) and the local summary statistics (e.g., the correlation between the local eigenvectors of the previous and current windows) for each window.
grMatrix C++ implementation to compute the genomic relationship matrix (grm) for a (sparse) input matrix as defined in Yang et al. (2011).
jaccardMatrix C++ implementation to compute the Jaccard similarity matrix for a (sparse) input matrix.
makeWindows Auxiliary function to generate a two-column matrix of windows to be used in the function 'fullscan'.
powerMethod C++ implementation of the power method (von Mises iteration) to compute the largest eigenvector of a dense input matrix.
selectVariants Auxiliary function to invert minor alleles and to select those variants/loci exceeding a minimal cutoff value.
sMatrix C++ implementation to compute the s-matrix (the weighted Jaccard similarity matrix) for a (sparse) input matrix as in the 'Stego' package: https://github.com/dschlauch/stego
testdata Simulated test data.